Bioinformatics Vol. 19 Suppl. 2 2003
pages ii246-ii255
© 2003 Oxford University Press
Flexible structure alignment by chaining aligned fragment pairs allowing twists
Program in Bioinformatics and Systems Biology, The Burnham Institute, La Jolla, CA 92037, USA
Received on March 17, 2003
; accepted on June 9, 2003
Motivation: Protein structures are flexible and undergo structural rearrangements as part of their function, and yet most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment.
Results: We have developed the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT), a new method for structural alignment of proteins. The FATCAT approach simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference protein. In contrast, currently existing flexible structure alignment programs treat the hinge detection as a post-process of a standard rigid body alignment. We illustrate the advantages of the FATCAT approach by several examples of comparison between proteins known to adopt different conformations, where the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges.
Contacts: adam{at}burnham.org
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Nigham, L. Tucker-Kellogg, I. Mihalek, C. Verma, and D. Hsu pFlexAna: detecting conformational changes in remotely related proteins Nucleic Acids Res., July 1, 2008; 36(suppl_2): W246 - W251. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Tsukihara, Y. Honda, R. Sakai, T. Watanabe, and T. Watanabe Mechanism for Oxidation of High-Molecular-Weight Substrates by a Fungal Versatile Peroxidase, MnP2 Appl. Envir. Microbiol., May 1, 2008; 74(9): 2873 - 2881. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. L. Hayes, B. L. Lytle, B. F. Volkman, and F. C. Peterson The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominately unstructured protein Protein Sci., March 1, 2008; 17(3): 571 - 576. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Occhino, F. Ghiotto, S. Soro, M. Mortarino, S. Bosi, M. Maffei, S. Bruno, M. Nardini, M. Figini, A. Tramontano, et al. Dissecting the Structural Determinants of the Interaction between the Human Cytomegalovirus UL18 Protein and the CD85j Immune Receptor J. Immunol., January 15, 2008; 180(2): 957 - 968. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. S. Dias, A. L. Macedo, G. C. Ferreira, F. C. Peterson, B. F. Volkman, and B. J. Goodfellow The First Structure from the SOUL/HBP Family of Heme-binding Proteins, Murine P22HBP J. Biol. Chem., October 20, 2006; 281(42): 31553 - 31561. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Ye and A. Godzik Multiple flexible structure alignment using partial order graphs Bioinformatics, May 15, 2005; 21(10): 2362 - 2369. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. L. Lytle, F. C. Peterson, S.-H. Qiu, M. Luo, Q. Zhao, J. L. Markley, and B. F. Volkman Solution Structure of a Ubiquitin-like Domain from Tubulin-binding Cofactor B J. Biol. Chem., November 5, 2004; 279(45): 46787 - 46793. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Ye and A. Godzik Database searching by flexible protein structure alignment Protein Sci., July 1, 2004; 13(7): 1841 - 1850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Ye and A. Godzik FATCAT: a web server for flexible structure comparison and structure similarity searching Nucleic Acids Res., July 1, 2004; 32(suppl_2): W582 - W585. [Abstract] [Full Text] [PDF]
|
|